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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttataattgtctccttatgatataaaatataccatcaaaatatctgcag

Basic information

species Oryza sativa
transcript LOC_Os08g25734.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G163437_T03 (Zea mays), 5'ss of exon 5
AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgc---tttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaa--tttataattgt------ctccttatgatataaaatataccatcaaaatatctgcag
| |||||  | ||||||||||| |||||||| |||||||| ||||||||||| |||||||||||  |||||||||| || |||||  |||||||||||||||||||   |||  | || | |||  |||||  |  |||  |||         | || ||| ||   ||||||||          |||  |||| ||   | | || ||||  |   | |||
AGGCTTATCTATATGATGGTTATTGGGAAGATATTGGTACAATTGAGGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCAATACCAGATTTCAGgtatgcacattttcacttct-cactgtgctgcagtagaaagttacaacgccgcatgcgtgtcaaatcttataatttcaattagtccctgctgatttagcgtttcccttcaatctgaatacag

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G068506_T03 (Zea mays), 5'ss of exon 5
AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttata--------attgtctccttatgatataaaatataccatcaaaatatctgcag
| |||||  |||||||||||||||||||||| || |||||||||| |||||| |||||||||||  |||||||||| || |||||  |||||||||||||||||||||||| || |  |||  |||||  | || |  ||       |  | |||| | || |  ||        |||   ||||  |||| ||   |   || | ||  |   | |||
AGGCTTATCTGTATGATGGTTACTGGGAAGATATCGGTACCATTGCGGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCAATACCAGATTTCAGgtatgctttcacttct--cactgtgctgcagttggaagttgcaacgctgcatgcatatcaagtcttacaatttcaattagttcctactgatttagtgttccccttaaatctgaatacag

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 5
AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgcttt-caatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttataattgtc-tccttatgatataaaatataccatcaaaatatctgcag
||||||||||||||||||| |||||||||||||||||||| |||||||| ||||||||||||||||||||||| || ||||||||||| || || ||||||||   | |  |   | |  |   |        |   ||  |  | |||| ||   |   |  || |  || |  |  |||||   | |   ||     || | |   |||||
AAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattatataggctatttaatatatccatcatattgacaaatgtatttcaacggtagtatattgtggttctgatgtttatgtgttcatgcattttggcatattgattgcag

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 5
AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttataattgtc-tccttatgatataaaatataccatcaaaatatctgcag
||||||||||||||||||| |||||||||||||||||||| || ||||| ||||||||||||||||||||||| || ||||||||||| || || ||||||||   |  | ||||  | |  |   |     |||  | | |   |||| ||  ||     ||| |  || |  |  |||||   | |    |     || | |   |||||
AAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATCGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACTTCAGgtaaattgcctatttg-atatatccatcatattgacaaatgt---atttcaatgatagtgttttgtggttctgatgtttatgtgttcatgcgttttggcatattgattgcag

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 5'ss of exon 4
AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttca--atttttacacctt--gctgtggctgaa-gattatggaatttgaagcatgtgaatttataattgtctccttatgatataaaatataccatcaaaatatctgcag
|||||||| | ||||||||||||||||||||||||||||| || |||||||| ||||| || ||||| ||||| || || || || || || ||||| |||||   |  |   |||  |||||  |    |||  ||||| |||||   || ||     || ||||||  | ||                                          
AAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATTTTAGgtacagtaaccgcattactacactctctattgtatctgaatgattacttaactt-----atctgaattcttgatgcag--------------------------------------

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 5
AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttcaatttttacaccttgctgtg-gctgaagattatggaatttgaagcatgtgaatttataattgtctc-cttatgatataaaatataccatcaaaatatctgcag-------------
||||||||||||||||||| |||||||||||||||||||| |||||||| || ||||| || ||| |||| || || || ||||| || ||||||||||||||   || ||       || |   ||||   |||   ||| ||   | ||   ||   |  | | | |||  | |  || ||||  |   |||   || || ||   |                 
AAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATTTCAGgtagttttacagcc----catcagactgtatactgtgaattttgatctctgtt-caacagtttctttcattaccacatttctgatgcagtttatgatattaatatggttttgaacttaaattgcag

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S2_392V6.1 (Physcomitrella patens), 5'ss of exon 5
AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttcaatttttacac---cttgctgtggctgaa----gattatggaatttgaagcatgtgaattta---taattgtctccttatgata-taaaatat-accatcaaaatat-ctgcag--------------------------------------------------------
|||| |||||||||||||| |||||||||||||| ||||| || ||||| ||||| || || ||| |||| || || || ||||| || |||||||||||||  |    ||    ||| |     |   |      | |    |||     | ||      |||  |   |    | |   || |||| || || |    ||| |  ||  |  ||| ||| ||                                                        
AAGCGTACTTGTATGATGGCTACTGGGAAGACATCGGTACTATCGAGGCTTTCTACAACGCGAATTTGGGCATCACCAAGAAGCCCGTGCCAGATTTCAGgtgagtagccagcaattagatgaattaaattcaatcgtattgtgatctgcaagttccttttatgacagcctcccttgaacttcgccttttgctaattgcttattattatttaggtatgctgtaggataatccactaaagcaatcattttttcgttaacatgctgctttttgcctcttcag

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S239_45V6.1 (Physcomitrella patens), 5'ss of exon 5
AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttataattgtctccttatgatataaaatataccatcaaaatatctgcag
|||| ||||||||||| || ||||||||||| ||||| || || || || ||||| ||||||||  | || || ||||| |||||||| || || |||||||  ||  ||  |    | |        ||   ||  | |||  |  | |    | |     ||||| ||  |||  || || |     ||||  || |     |||    
AAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACTTCAGgtgagcactcggt----agaatgatgaatgtaagacaaatatacagctagggcaacgctt-cttata-ttccctctctagga-accgcttatatgattactcattct----

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 5'ss of exon 5
AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttataattgtctccttatgatataaaatataccatcaaaatatctgcag
||||||| ||||| ||||| ||||||||||| ||||| || ||||| |||||||| ||||| |||||||| || || || || ||||| || ||||||||||  | | ||    ||   | ||  |      |      | | |  ||||    |  | |   || || ||| | | | | |  |      |   ||| |   |       
AAGCTTATTTGTACGATGGCTACTGGGAAGATATTGGAACTATTGAAGCATTCTACAATGCCAATCTGGGCATCACTAAGAAACCTGTTCCTGATTTCAGgtgagttatcttccttcttatctctcataaattct--gctctaggctttgttcta-ataatggtagaaatgtgtgcgt-taacttgg--cttgttatcgactgact-----

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|87012877|gb|CI297104.1|CI297104
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|29681077|gb|CB677352.1|CB677352
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|58606969|gb|CK035002.1|CK035002
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACGACGTTGCCT
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGAC-AC-TTGCCT
EST: gi|33681770|gb|CF310009.1|CF310009
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|58678083|gb|CK066770.1|CK066770
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATA
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATA
EST: gi|29612859|gb|CB617872.1|CB617872
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|38472262|gb|CF956393.1|CF956393
EST:     GAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: GAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|29671442|gb|CB667717.1|CB667717
EST:     TTTTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|88586416|gb|CI704115.1|CI704115
EST:     TCCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TCTCTATGACCGGTCTGCTCCAATTTATANACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|29660395|gb|CB656670.1|CB656670
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|29614233|gb|CB619246.1|CB619246
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCCTCGACACTTGCCTT
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACC-TCGACACTTGCCT-
EST: gi|58652879|gb|CK041559.1|CK041559
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACA
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACA
EST: gi|58675386|gb|CK064073.1|CK064073
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|88584775|gb|CI702352.1|CI702352
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAACCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGAC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGAC
EST: gi|86831383|gb|CI299441.1|CI299441
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTG
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTG
EST: gi|29620180|gb|CB625192.1|CB625192
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 764

AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT




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